Starting phenix.real_space_refine on Tue Dec 31 12:54:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bx7_16311/12_2024/8bx7_16311.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bx7_16311/12_2024/8bx7_16311.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8bx7_16311/12_2024/8bx7_16311.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bx7_16311/12_2024/8bx7_16311.map" model { file = "/net/cci-nas-00/data/ceres_data/8bx7_16311/12_2024/8bx7_16311.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bx7_16311/12_2024/8bx7_16311.cif" } resolution = 2.76 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 80 5.16 5 C 10046 2.51 5 N 2644 2.21 5 O 2867 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 43 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 15637 Number of models: 1 Model: "" Number of chains: 5 Chain: "D" Number of atoms: 3561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 465, 3561 Classifications: {'peptide': 465} Incomplete info: {'backbone_only': 26, 'truncation_to_alanine': 35} Link IDs: {'PTRANS': 14, 'TRANS': 450} Chain breaks: 2 Unresolved non-hydrogen bonds: 243 Unresolved non-hydrogen angles: 328 Unresolved non-hydrogen dihedrals: 178 Unresolved non-hydrogen chiralities: 46 Planarities with less than four sites: {'GLN:plan1': 6, 'TYR:plan': 3, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 125 Chain: "A" Number of atoms: 3916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 511, 3916 Classifications: {'peptide': 511} Incomplete info: {'backbone_only': 48, 'truncation_to_alanine': 12} Link IDs: {'PTRANS': 15, 'TRANS': 495} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 273 Unresolved non-hydrogen angles: 370 Unresolved non-hydrogen dihedrals: 184 Unresolved non-hydrogen chiralities: 66 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 117 Chain: "B" Number of atoms: 3954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 3954 Classifications: {'peptide': 505} Incomplete info: {'backbone_only': 41, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 14, 'TRANS': 490} Chain breaks: 1 Unresolved non-hydrogen bonds: 189 Unresolved non-hydrogen angles: 264 Unresolved non-hydrogen dihedrals: 121 Unresolved non-hydrogen chiralities: 54 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 1, 'ASP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 82 Chain: "C" Number of atoms: 3946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 3946 Classifications: {'peptide': 513} Incomplete info: {'backbone_only': 53, 'truncation_to_alanine': 10} Link IDs: {'PTRANS': 16, 'TRANS': 496} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 266 Unresolved non-hydrogen angles: 369 Unresolved non-hydrogen dihedrals: 172 Unresolved non-hydrogen chiralities: 74 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 4, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 103 Chain: "E" Number of atoms: 260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 260 Classifications: {'peptide': 65} Incomplete info: {'backbone_only': 60} Link IDs: {'TRANS': 64} Unresolved non-hydrogen bonds: 267 Unresolved non-hydrogen angles: 382 Unresolved non-hydrogen dihedrals: 166 Unresolved non-hydrogen chiralities: 75 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 3, 'ASP:plan': 7, 'PHE:plan': 3, 'GLU:plan': 10, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 151 Time building chain proxies: 10.20, per 1000 atoms: 0.65 Number of scatterers: 15637 At special positions: 0 Unit cell: (94.86, 122.4, 176.46, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 80 16.00 O 2867 8.00 N 2644 7.00 C 10046 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.38 Conformation dependent library (CDL) restraints added in 2.5 seconds 4078 Ramachandran restraints generated. 2039 Oldfield, 0 Emsley, 2039 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3440 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 11 sheets defined 66.0% alpha, 5.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.60 Creating SS restraints... Processing helix chain 'D' and resid 769 through 794 Proline residue: D 789 - end of helix Processing helix chain 'D' and resid 798 through 819 removed outlier: 4.694A pdb=" N HIS D 803 " --> pdb=" O PRO D 799 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N LEU D 804 " --> pdb=" O ASP D 800 " (cutoff:3.500A) Processing helix chain 'D' and resid 841 through 848 removed outlier: 4.176A pdb=" N VAL D 847 " --> pdb=" O ARG D 843 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS D 848 " --> pdb=" O ASN D 844 " (cutoff:3.500A) Processing helix chain 'D' and resid 849 through 855 Processing helix chain 'D' and resid 872 through 877 removed outlier: 3.953A pdb=" N ARG D 876 " --> pdb=" O ASN D 872 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU D 877 " --> pdb=" O PRO D 873 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 872 through 877' Processing helix chain 'D' and resid 882 through 897 removed outlier: 3.985A pdb=" N PHE D 886 " --> pdb=" O LYS D 882 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE D 887 " --> pdb=" O TYR D 883 " (cutoff:3.500A) Processing helix chain 'D' and resid 900 through 931 removed outlier: 3.862A pdb=" N ARG D 904 " --> pdb=" O ALA D 900 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N VAL D 905 " --> pdb=" O TYR D 901 " (cutoff:3.500A) Processing helix chain 'D' and resid 944 through 957 removed outlier: 3.693A pdb=" N ARG D 948 " --> pdb=" O ASN D 944 " (cutoff:3.500A) Processing helix chain 'D' and resid 971 through 1021 removed outlier: 4.225A pdb=" N GLY D 976 " --> pdb=" O ILE D 972 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N LEU D 977 " --> pdb=" O VAL D 973 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N GLY D1003 " --> pdb=" O ALA D 999 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N GLN D1004 " --> pdb=" O ALA D1000 " (cutoff:3.500A) Processing helix chain 'D' and resid 1024 through 1040 Processing helix chain 'D' and resid 1047 through 1053 removed outlier: 4.033A pdb=" N GLN D1053 " --> pdb=" O GLU D1049 " (cutoff:3.500A) Processing helix chain 'D' and resid 1055 through 1067 Processing helix chain 'D' and resid 1067 through 1073 removed outlier: 4.071A pdb=" N VAL D1071 " --> pdb=" O ASN D1067 " (cutoff:3.500A) Processing helix chain 'D' and resid 1081 through 1091 removed outlier: 4.075A pdb=" N ILE D1085 " --> pdb=" O ASP D1081 " (cutoff:3.500A) Processing helix chain 'D' and resid 1143 through 1149 removed outlier: 3.784A pdb=" N LEU D1148 " --> pdb=" O ILE D1145 " (cutoff:3.500A) Processing helix chain 'D' and resid 1172 through 1182 removed outlier: 4.085A pdb=" N HIS D1182 " --> pdb=" O GLU D1178 " (cutoff:3.500A) Processing helix chain 'D' and resid 1183 through 1203 removed outlier: 3.856A pdb=" N LEU D1189 " --> pdb=" O GLU D1185 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ASN D1201 " --> pdb=" O MET D1197 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ASN D1202 " --> pdb=" O LEU D1198 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LYS D1203 " --> pdb=" O ARG D1199 " (cutoff:3.500A) Processing helix chain 'D' and resid 1238 through 1265 Processing helix chain 'A' and resid 160 through 180 removed outlier: 3.722A pdb=" N LEU A 172 " --> pdb=" O PHE A 168 " (cutoff:3.500A) Proline residue: A 173 - end of helix Processing helix chain 'A' and resid 181 through 187 removed outlier: 3.512A pdb=" N PHE A 187 " --> pdb=" O ALA A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 218 removed outlier: 3.850A pdb=" N GLN A 191 " --> pdb=" O PHE A 187 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N GLU A 196 " --> pdb=" O SER A 192 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N TYR A 197 " --> pdb=" O ASP A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 241 Processing helix chain 'A' and resid 244 through 249 Processing helix chain 'A' and resid 255 through 261 removed outlier: 3.950A pdb=" N ILE A 259 " --> pdb=" O ASP A 255 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N LYS A 260 " --> pdb=" O LEU A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 271 removed outlier: 3.508A pdb=" N ILE A 268 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ASN A 271 " --> pdb=" O ILE A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 288 removed outlier: 3.581A pdb=" N PHE A 282 " --> pdb=" O ARG A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 323 Processing helix chain 'A' and resid 342 through 360 removed outlier: 3.924A pdb=" N SER A 350 " --> pdb=" O LYS A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 402 removed outlier: 3.644A pdb=" N PHE A 374 " --> pdb=" O ASP A 370 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE A 375 " --> pdb=" O SER A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 421 Processing helix chain 'A' and resid 425 through 442 Processing helix chain 'A' and resid 447 through 452 removed outlier: 3.507A pdb=" N LEU A 452 " --> pdb=" O GLU A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 468 Processing helix chain 'A' and resid 469 through 475 Processing helix chain 'A' and resid 482 through 491 Processing helix chain 'A' and resid 576 through 583 Processing helix chain 'A' and resid 586 through 604 Processing helix chain 'A' and resid 619 through 665 Processing helix chain 'B' and resid 160 through 180 Proline residue: B 173 - end of helix Processing helix chain 'B' and resid 181 through 187 Processing helix chain 'B' and resid 194 through 216 removed outlier: 3.616A pdb=" N ASP B 202 " --> pdb=" O TRP B 198 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N TYR B 203 " --> pdb=" O LEU B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 219 No H-bonds generated for 'chain 'B' and resid 217 through 219' Processing helix chain 'B' and resid 233 through 241 Processing helix chain 'B' and resid 242 through 250 removed outlier: 3.525A pdb=" N LEU B 246 " --> pdb=" O PHE B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 259 removed outlier: 3.828A pdb=" N ILE B 259 " --> pdb=" O LEU B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 274 removed outlier: 3.612A pdb=" N ILE B 268 " --> pdb=" O TYR B 265 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU B 270 " --> pdb=" O GLU B 267 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ASN B 271 " --> pdb=" O ILE B 268 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ARG B 272 " --> pdb=" O ARG B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 290 removed outlier: 4.255A pdb=" N MET B 279 " --> pdb=" O ARG B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 324 removed outlier: 3.784A pdb=" N ILE B 323 " --> pdb=" O ILE B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 358 removed outlier: 3.932A pdb=" N SER B 350 " --> pdb=" O LYS B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 402 removed outlier: 3.605A pdb=" N PHE B 375 " --> pdb=" O SER B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 422 Processing helix chain 'B' and resid 425 through 442 Processing helix chain 'B' and resid 447 through 453 Processing helix chain 'B' and resid 456 through 468 Processing helix chain 'B' and resid 470 through 474 Processing helix chain 'B' and resid 482 through 492 removed outlier: 3.546A pdb=" N GLU B 488 " --> pdb=" O GLY B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 548 removed outlier: 3.894A pdb=" N ILE B 547 " --> pdb=" O GLY B 543 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N LEU B 548 " --> pdb=" O GLU B 544 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 543 through 548' Processing helix chain 'B' and resid 576 through 584 Processing helix chain 'B' and resid 586 through 605 removed outlier: 3.601A pdb=" N GLY B 605 " --> pdb=" O LEU B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 664 Processing helix chain 'C' and resid 161 through 187 Proline residue: C 173 - end of helix removed outlier: 5.129A pdb=" N ILE C 182 " --> pdb=" O TRP C 178 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ALA C 183 " --> pdb=" O THR C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 194 Processing helix chain 'C' and resid 196 through 218 Processing helix chain 'C' and resid 230 through 239 Processing helix chain 'C' and resid 241 through 252 removed outlier: 3.762A pdb=" N LYS C 245 " --> pdb=" O THR C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 256 No H-bonds generated for 'chain 'C' and resid 254 through 256' Processing helix chain 'C' and resid 257 through 262 Processing helix chain 'C' and resid 266 through 271 removed outlier: 4.210A pdb=" N ASN C 271 " --> pdb=" O ILE C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 290 removed outlier: 3.582A pdb=" N MET C 279 " --> pdb=" O ARG C 275 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLU C 287 " --> pdb=" O PHE C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 324 removed outlier: 3.722A pdb=" N PHE C 296 " --> pdb=" O TYR C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 344 through 359 Processing helix chain 'C' and resid 369 through 422 removed outlier: 4.856A pdb=" N ALA C 404 " --> pdb=" O ASN C 400 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N ARG C 405 " --> pdb=" O MET C 401 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 442 Processing helix chain 'C' and resid 447 through 454 removed outlier: 3.789A pdb=" N TYR C 454 " --> pdb=" O GLU C 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 456 through 468 Processing helix chain 'C' and resid 476 through 480 removed outlier: 3.508A pdb=" N ALA C 479 " --> pdb=" O ARG C 476 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N ASP C 480 " --> pdb=" O ILE C 477 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 476 through 480' Processing helix chain 'C' and resid 482 through 491 Processing helix chain 'C' and resid 576 through 584 Processing helix chain 'C' and resid 586 through 604 removed outlier: 3.964A pdb=" N LYS C 590 " --> pdb=" O TYR C 586 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N GLY C 591 " --> pdb=" O PRO C 587 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASP C 604 " --> pdb=" O ILE C 600 " (cutoff:3.500A) Processing helix chain 'C' and resid 619 through 670 removed outlier: 3.523A pdb=" N ARG C 641 " --> pdb=" O THR C 637 " (cutoff:3.500A) Proline residue: C 666 - end of helix Processing helix chain 'E' and resid 86 through 94 Processing helix chain 'E' and resid 104 through 113 removed outlier: 3.957A pdb=" N HIS E 108 " --> pdb=" O ALA E 104 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N THR E 111 " --> pdb=" O ARG E 107 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ASN E 112 " --> pdb=" O HIS E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 130 Processing helix chain 'E' and resid 139 through 148 Processing sheet with id=AA1, first strand: chain 'D' and resid 829 through 831 removed outlier: 3.685A pdb=" N PHE D 829 " --> pdb=" O ILE D 836 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 1093 through 1097 removed outlier: 6.835A pdb=" N ASN D1167 " --> pdb=" O GLN D1117 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 1101 through 1104 removed outlier: 6.513A pdb=" N TYR D1102 " --> pdb=" O ALA D1162 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ALA D1162 " --> pdb=" O TYR D1102 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ASN D1159 " --> pdb=" O LEU D1124 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N VAL D1121 " --> pdb=" O THR D1135 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N THR D1135 " --> pdb=" O VAL D1121 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N VAL D1123 " --> pdb=" O LEU D1133 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 494 through 496 Processing sheet with id=AA5, first strand: chain 'A' and resid 503 through 505 removed outlier: 6.490A pdb=" N TYR A 503 " --> pdb=" O SER A 565 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N SER A 565 " --> pdb=" O TYR A 503 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ASN A 562 " --> pdb=" O VAL A 525 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N VAL A 534 " --> pdb=" O VAL A 524 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 494 through 496 Processing sheet with id=AA7, first strand: chain 'B' and resid 532 through 534 removed outlier: 3.832A pdb=" N VAL B 534 " --> pdb=" O VAL B 524 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASN B 562 " --> pdb=" O VAL B 525 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 222 through 223 Processing sheet with id=AA9, first strand: chain 'C' and resid 494 through 498 Processing sheet with id=AB1, first strand: chain 'C' and resid 503 through 505 removed outlier: 6.128A pdb=" N TYR C 503 " --> pdb=" O SER C 565 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N SER C 565 " --> pdb=" O TYR C 503 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N CYS C 505 " --> pdb=" O ILE C 563 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL C 534 " --> pdb=" O VAL C 524 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 100 through 102 1018 hydrogen bonds defined for protein. 2967 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.55 Time building geometry restraints manager: 4.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5070 1.34 - 1.46: 3867 1.46 - 1.58: 6904 1.58 - 1.70: 0 1.70 - 1.82: 134 Bond restraints: 15975 Sorted by residual: bond pdb=" N ILE D1109 " pdb=" CA ILE D1109 " ideal model delta sigma weight residual 1.461 1.498 -0.037 1.19e-02 7.06e+03 9.68e+00 bond pdb=" N GLU D1108 " pdb=" CA GLU D1108 " ideal model delta sigma weight residual 1.454 1.490 -0.036 1.18e-02 7.18e+03 9.40e+00 bond pdb=" N GLU D1112 " pdb=" CA GLU D1112 " ideal model delta sigma weight residual 1.454 1.492 -0.039 1.34e-02 5.57e+03 8.29e+00 bond pdb=" N ARG D1111 " pdb=" CA ARG D1111 " ideal model delta sigma weight residual 1.459 1.488 -0.028 1.21e-02 6.83e+03 5.54e+00 bond pdb=" N ARG D1156 " pdb=" CA ARG D1156 " ideal model delta sigma weight residual 1.456 1.485 -0.029 1.25e-02 6.40e+03 5.39e+00 ... (remaining 15970 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 21147 2.05 - 4.11: 332 4.11 - 6.16: 58 6.16 - 8.21: 8 8.21 - 10.27: 7 Bond angle restraints: 21552 Sorted by residual: angle pdb=" C LYS B 506 " pdb=" CA LYS B 506 " pdb=" CB LYS B 506 " ideal model delta sigma weight residual 116.63 110.22 6.41 1.16e+00 7.43e-01 3.05e+01 angle pdb=" N GLU D1112 " pdb=" CA GLU D1112 " pdb=" C GLU D1112 " ideal model delta sigma weight residual 110.19 115.77 -5.58 1.24e+00 6.50e-01 2.03e+01 angle pdb=" CB LYS C 453 " pdb=" CG LYS C 453 " pdb=" CD LYS C 453 " ideal model delta sigma weight residual 111.30 121.57 -10.27 2.30e+00 1.89e-01 1.99e+01 angle pdb=" N ILE D 958 " pdb=" CA ILE D 958 " pdb=" C ILE D 958 " ideal model delta sigma weight residual 113.53 109.75 3.78 9.80e-01 1.04e+00 1.49e+01 angle pdb=" N THR C 359 " pdb=" CA THR C 359 " pdb=" C THR C 359 " ideal model delta sigma weight residual 110.35 105.79 4.56 1.38e+00 5.25e-01 1.09e+01 ... (remaining 21547 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.33: 7992 17.33 - 34.67: 878 34.67 - 52.00: 202 52.00 - 69.34: 50 69.34 - 86.67: 13 Dihedral angle restraints: 9135 sinusoidal: 3536 harmonic: 5599 Sorted by residual: dihedral pdb=" CA TYR B 568 " pdb=" C TYR B 568 " pdb=" N SER B 569 " pdb=" CA SER B 569 " ideal model delta harmonic sigma weight residual 180.00 156.67 23.33 0 5.00e+00 4.00e-02 2.18e+01 dihedral pdb=" CA ILE C 516 " pdb=" C ILE C 516 " pdb=" N ILE C 517 " pdb=" CA ILE C 517 " ideal model delta harmonic sigma weight residual 180.00 -157.17 -22.83 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" CA TRP C 198 " pdb=" C TRP C 198 " pdb=" N LEU C 199 " pdb=" CA LEU C 199 " ideal model delta harmonic sigma weight residual 180.00 157.27 22.73 0 5.00e+00 4.00e-02 2.07e+01 ... (remaining 9132 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1507 0.036 - 0.072: 583 0.072 - 0.108: 150 0.108 - 0.144: 31 0.144 - 0.179: 4 Chirality restraints: 2275 Sorted by residual: chirality pdb=" CA MET B 592 " pdb=" N MET B 592 " pdb=" C MET B 592 " pdb=" CB MET B 592 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.05e-01 chirality pdb=" CA ILE C 517 " pdb=" N ILE C 517 " pdb=" C ILE C 517 " pdb=" CB ILE C 517 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 6.00e-01 chirality pdb=" CB ILE B 309 " pdb=" CA ILE B 309 " pdb=" CG1 ILE B 309 " pdb=" CG2 ILE B 309 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.72e-01 ... (remaining 2272 not shown) Planarity restraints: 2780 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 773 " 0.022 2.00e-02 2.50e+03 1.97e-02 9.74e+00 pdb=" CG TRP D 773 " -0.054 2.00e-02 2.50e+03 pdb=" CD1 TRP D 773 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP D 773 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP D 773 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 773 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 773 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 773 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 773 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP D 773 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 364 " -0.039 5.00e-02 4.00e+02 5.96e-02 5.69e+00 pdb=" N PRO A 365 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO A 365 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 365 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY D1107 " 0.010 2.00e-02 2.50e+03 2.03e-02 4.12e+00 pdb=" C GLY D1107 " -0.035 2.00e-02 2.50e+03 pdb=" O GLY D1107 " 0.013 2.00e-02 2.50e+03 pdb=" N GLU D1108 " 0.012 2.00e-02 2.50e+03 ... (remaining 2777 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1749 2.75 - 3.29: 15908 3.29 - 3.82: 26481 3.82 - 4.36: 29402 4.36 - 4.90: 50676 Nonbonded interactions: 124216 Sorted by model distance: nonbonded pdb=" OD2 ASP B 370 " pdb=" NH2 ARG C 342 " model vdw 2.209 3.120 nonbonded pdb=" O PHE B 214 " pdb=" OG1 THR B 217 " model vdw 2.210 3.040 nonbonded pdb=" OD2 ASP C 188 " pdb=" NZ LYS C 321 " model vdw 2.215 3.120 nonbonded pdb=" NH2 ARG D1025 " pdb=" OD1 ASN D1029 " model vdw 2.221 3.120 nonbonded pdb=" OH TYR A 209 " pdb=" O ARG A 272 " model vdw 2.223 3.040 ... (remaining 124211 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 154 through 359 or (resid 360 and (name N or name CA or na \ me C or name O or name CB )) or resid 361 through 362 or (resid 363 and (name N \ or name CA or name C or name O or name CB )) or resid 364 through 572 or (resid \ 573 and (name N or name CA or name C or name O or name CB )) or resid 574 throug \ h 601 or (resid 602 through 604 and (name N or name CA or name C or name O or na \ me CB )) or (resid 605 through 613 and (name N or name CA or name C or name O or \ name CB )) or resid 624 through 664)) selection = (chain 'B' and (resid 154 through 215 or (resid 216 and (name N or name CA or na \ me C or name O or name CB or name CG )) or resid 217 through 277 or (resid 278 a \ nd (name N or name CA or name C or name O or name CB or name CG )) or resid 279 \ through 359 or (resid 360 and (name N or name CA or name C or name O or name CB \ )) or resid 361 through 442 or (resid 443 and (name N or name CA or name C or na \ me O or name CB )) or resid 444 through 457 or (resid 458 and (name N or name CA \ or name C or name O or name CB or name CG )) or resid 459 through 511 or (resid \ 512 and (name N or name CA or name C or name O or name CB )) or resid 513 throu \ gh 548 or (resid 549 and (name N or name CA or name C or name O or name CB )) or \ resid 550 through 553 or (resid 554 through 555 and (name N or name CA or name \ C or name O or name CB )) or resid 556 through 561 or (resid 562 and (name N or \ name CA or name C or name O or name CB )) or resid 563 through 575 or (resid 576 \ and (name N or name CA or name C or name O or name CB or name CG or name CD )) \ or resid 577 through 601 or (resid 602 through 604 and (name N or name CA or nam \ e C or name O or name CB )) or resid 605 or (resid 606 through 613 and (name N o \ r name CA or name C or name O or name CB )) or resid 624 through 664)) selection = (chain 'C' and (resid 154 through 215 or (resid 216 and (name N or name CA or na \ me C or name O or name CB or name CG )) or resid 217 through 277 or (resid 278 a \ nd (name N or name CA or name C or name O or name CB or name CG )) or resid 279 \ through 362 or (resid 363 and (name N or name CA or name C or name O or name CB \ )) or resid 364 through 442 or (resid 443 and (name N or name CA or name C or na \ me O or name CB )) or resid 444 through 457 or (resid 458 and (name N or name CA \ or name C or name O or name CB or name CG )) or resid 459 through 511 or (resid \ 512 and (name N or name CA or name C or name O or name CB )) or resid 513 throu \ gh 548 or (resid 549 and (name N or name CA or name C or name O or name CB )) or \ resid 550 through 561 or (resid 562 and (name N or name CA or name C or name O \ or name CB )) or resid 563 through 572 or (resid 573 and (name N or name CA or n \ ame C or name O or name CB )) or resid 574 through 575 or (resid 576 and (name N \ or name CA or name C or name O or name CB or name CG or name CD )) or resid 577 \ through 603 or (resid 604 and (name N or name CA or name C or name O or name CB \ )) or (resid 605 through 613 and (name N or name CA or name C or name O or name \ CB )) or resid 624 through 664)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.690 Check model and map are aligned: 0.110 Set scattering table: 0.170 Process input model: 38.100 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 15975 Z= 0.203 Angle : 0.659 10.266 21552 Z= 0.377 Chirality : 0.040 0.179 2275 Planarity : 0.004 0.060 2780 Dihedral : 15.281 86.671 5695 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.35 % Favored : 94.61 % Rotamer: Outliers : 1.92 % Allowed : 19.51 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.20), residues: 2039 helix: 1.46 (0.15), residues: 1316 sheet: -0.91 (0.67), residues: 68 loop : -1.54 (0.25), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP D 773 HIS 0.005 0.001 HIS A 310 PHE 0.014 0.001 PHE A 421 TYR 0.017 0.001 TYR D 810 ARG 0.004 0.000 ARG A 269 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4078 Ramachandran restraints generated. 2039 Oldfield, 0 Emsley, 2039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4078 Ramachandran restraints generated. 2039 Oldfield, 0 Emsley, 2039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 181 time to evaluate : 2.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 MET cc_start: 0.7455 (tmt) cc_final: 0.6753 (ttp) REVERT: B 449 ARG cc_start: 0.8194 (mtt90) cc_final: 0.7927 (mpt-90) REVERT: B 595 GLU cc_start: 0.8744 (OUTLIER) cc_final: 0.8526 (mp0) REVERT: C 513 GLU cc_start: 0.8375 (mp0) cc_final: 0.7906 (mp0) outliers start: 30 outliers final: 13 residues processed: 203 average time/residue: 1.1224 time to fit residues: 258.3213 Evaluate side-chains 174 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 160 time to evaluate : 1.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 779 LEU Chi-restraints excluded: chain D residue 812 CYS Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain D residue 1115 ILE Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 595 GLU Chi-restraints excluded: chain C residue 258 TYR Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 571 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 3.9990 chunk 154 optimal weight: 5.9990 chunk 85 optimal weight: 0.6980 chunk 52 optimal weight: 0.8980 chunk 104 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 159 optimal weight: 4.9990 chunk 61 optimal weight: 0.6980 chunk 97 optimal weight: 0.0040 chunk 119 optimal weight: 2.9990 chunk 185 optimal weight: 2.9990 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 442 ASN B 224 GLN B 284 GLN B 417 GLN B 494 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.0763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 15975 Z= 0.185 Angle : 0.550 8.201 21552 Z= 0.294 Chirality : 0.041 0.147 2275 Planarity : 0.004 0.055 2780 Dihedral : 5.181 55.228 2278 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.30 % Favored : 94.65 % Rotamer: Outliers : 3.58 % Allowed : 17.47 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.20), residues: 2039 helix: 1.73 (0.15), residues: 1323 sheet: -0.98 (0.68), residues: 63 loop : -1.55 (0.24), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP D 773 HIS 0.005 0.001 HIS A 310 PHE 0.017 0.001 PHE A 421 TYR 0.014 0.001 TYR D 810 ARG 0.007 0.000 ARG A 269 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4078 Ramachandran restraints generated. 2039 Oldfield, 0 Emsley, 2039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4078 Ramachandran restraints generated. 2039 Oldfield, 0 Emsley, 2039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 180 time to evaluate : 1.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 828 GLN cc_start: 0.6226 (OUTLIER) cc_final: 0.5731 (pt0) REVERT: D 1049 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.8050 (mp0) REVERT: B 258 TYR cc_start: 0.5763 (OUTLIER) cc_final: 0.4983 (t80) REVERT: B 279 MET cc_start: 0.7622 (ppp) cc_final: 0.7328 (ptm) REVERT: B 407 GLU cc_start: 0.7792 (mt-10) cc_final: 0.7577 (mm-30) REVERT: B 415 ILE cc_start: 0.8366 (tp) cc_final: 0.8128 (tp) REVERT: B 449 ARG cc_start: 0.8195 (OUTLIER) cc_final: 0.7974 (mpt-90) outliers start: 56 outliers final: 20 residues processed: 219 average time/residue: 1.0739 time to fit residues: 267.5855 Evaluate side-chains 185 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 161 time to evaluate : 1.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 779 LEU Chi-restraints excluded: chain D residue 812 CYS Chi-restraints excluded: chain D residue 828 GLN Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain D residue 1049 GLU Chi-restraints excluded: chain D residue 1115 ILE Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 258 TYR Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 318 SER Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 449 ARG Chi-restraints excluded: chain B residue 577 ASP Chi-restraints excluded: chain C residue 258 TYR Chi-restraints excluded: chain C residue 428 MET Chi-restraints excluded: chain C residue 449 ARG Chi-restraints excluded: chain C residue 503 TYR Chi-restraints excluded: chain C residue 504 ILE Chi-restraints excluded: chain C residue 571 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 102 optimal weight: 0.6980 chunk 57 optimal weight: 0.6980 chunk 154 optimal weight: 3.9990 chunk 126 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 185 optimal weight: 0.8980 chunk 200 optimal weight: 9.9990 chunk 165 optimal weight: 0.8980 chunk 184 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 148 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D1167 ASN B 284 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.1040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15975 Z= 0.197 Angle : 0.539 9.475 21552 Z= 0.287 Chirality : 0.041 0.163 2275 Planarity : 0.004 0.054 2780 Dihedral : 4.853 57.229 2270 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.00 % Favored : 94.95 % Rotamer: Outliers : 3.97 % Allowed : 17.85 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.20), residues: 2039 helix: 1.84 (0.15), residues: 1323 sheet: -0.69 (0.69), residues: 61 loop : -1.49 (0.24), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP D 773 HIS 0.005 0.001 HIS A 310 PHE 0.018 0.001 PHE A 421 TYR 0.035 0.001 TYR C 503 ARG 0.005 0.000 ARG A 269 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4078 Ramachandran restraints generated. 2039 Oldfield, 0 Emsley, 2039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4078 Ramachandran restraints generated. 2039 Oldfield, 0 Emsley, 2039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 178 time to evaluate : 2.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 828 GLN cc_start: 0.6199 (OUTLIER) cc_final: 0.5737 (pt0) REVERT: D 1049 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.8116 (mp0) REVERT: B 222 LEU cc_start: 0.7763 (OUTLIER) cc_final: 0.7191 (pp) REVERT: B 258 TYR cc_start: 0.5856 (OUTLIER) cc_final: 0.5064 (t80) REVERT: B 407 GLU cc_start: 0.7780 (mt-10) cc_final: 0.7564 (mm-30) REVERT: B 415 ILE cc_start: 0.8410 (tp) cc_final: 0.8143 (tp) REVERT: C 297 ARG cc_start: 0.8154 (ttt180) cc_final: 0.7736 (ptt180) outliers start: 62 outliers final: 27 residues processed: 219 average time/residue: 1.0718 time to fit residues: 266.9153 Evaluate side-chains 191 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 160 time to evaluate : 1.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 779 LEU Chi-restraints excluded: chain D residue 812 CYS Chi-restraints excluded: chain D residue 828 GLN Chi-restraints excluded: chain D residue 837 THR Chi-restraints excluded: chain D residue 980 PHE Chi-restraints excluded: chain D residue 1049 GLU Chi-restraints excluded: chain D residue 1115 ILE Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 258 TYR Chi-restraints excluded: chain B residue 287 GLU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 318 SER Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 530 ILE Chi-restraints excluded: chain C residue 258 TYR Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 428 MET Chi-restraints excluded: chain C residue 449 ARG Chi-restraints excluded: chain C residue 504 ILE Chi-restraints excluded: chain C residue 571 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 183 optimal weight: 2.9990 chunk 139 optimal weight: 2.9990 chunk 96 optimal weight: 10.0000 chunk 20 optimal weight: 4.9990 chunk 88 optimal weight: 0.9990 chunk 124 optimal weight: 4.9990 chunk 186 optimal weight: 0.6980 chunk 197 optimal weight: 7.9990 chunk 97 optimal weight: 4.9990 chunk 176 optimal weight: 0.9990 chunk 53 optimal weight: 0.5980 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 GLN B 284 GLN B 494 GLN C 191 GLN C 294 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.1229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.099 15975 Z= 0.253 Angle : 0.558 9.981 21552 Z= 0.295 Chirality : 0.042 0.160 2275 Planarity : 0.004 0.054 2780 Dihedral : 4.875 59.527 2268 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.59 % Favored : 94.36 % Rotamer: Outliers : 4.61 % Allowed : 18.11 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.19), residues: 2039 helix: 1.86 (0.15), residues: 1317 sheet: -0.61 (0.66), residues: 66 loop : -1.46 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP D 773 HIS 0.005 0.001 HIS A 310 PHE 0.018 0.001 PHE A 421 TYR 0.026 0.001 TYR D 810 ARG 0.005 0.000 ARG A 269 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4078 Ramachandran restraints generated. 2039 Oldfield, 0 Emsley, 2039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4078 Ramachandran restraints generated. 2039 Oldfield, 0 Emsley, 2039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 172 time to evaluate : 1.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 828 GLN cc_start: 0.6184 (OUTLIER) cc_final: 0.5722 (pt0) REVERT: D 893 LEU cc_start: 0.9074 (tp) cc_final: 0.8830 (tt) REVERT: D 993 MET cc_start: 0.9147 (mmm) cc_final: 0.8929 (tpt) REVERT: B 222 LEU cc_start: 0.7814 (OUTLIER) cc_final: 0.7305 (pp) REVERT: B 258 TYR cc_start: 0.5906 (OUTLIER) cc_final: 0.5156 (t80) REVERT: B 407 GLU cc_start: 0.7840 (mt-10) cc_final: 0.7522 (mm-30) REVERT: B 415 ILE cc_start: 0.8494 (tp) cc_final: 0.8262 (tp) REVERT: C 297 ARG cc_start: 0.8282 (ttt180) cc_final: 0.7832 (ptt180) outliers start: 72 outliers final: 37 residues processed: 222 average time/residue: 1.0249 time to fit residues: 259.2690 Evaluate side-chains 200 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 160 time to evaluate : 1.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 779 LEU Chi-restraints excluded: chain D residue 812 CYS Chi-restraints excluded: chain D residue 828 GLN Chi-restraints excluded: chain D residue 837 THR Chi-restraints excluded: chain D residue 980 PHE Chi-restraints excluded: chain D residue 1115 ILE Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 258 TYR Chi-restraints excluded: chain B residue 287 GLU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 318 SER Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 530 ILE Chi-restraints excluded: chain B residue 577 ASP Chi-restraints excluded: chain B residue 599 GLN Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 258 TYR Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 428 MET Chi-restraints excluded: chain C residue 449 ARG Chi-restraints excluded: chain C residue 504 ILE Chi-restraints excluded: chain C residue 512 ARG Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 571 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 164 optimal weight: 0.7980 chunk 111 optimal weight: 0.0770 chunk 2 optimal weight: 2.9990 chunk 146 optimal weight: 8.9990 chunk 81 optimal weight: 0.9990 chunk 168 optimal weight: 7.9990 chunk 136 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 100 optimal weight: 0.3980 chunk 176 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 overall best weight: 0.6542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 891 ASN B 284 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.1335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 15975 Z= 0.177 Angle : 0.532 9.209 21552 Z= 0.280 Chirality : 0.041 0.205 2275 Planarity : 0.003 0.055 2780 Dihedral : 4.789 59.636 2268 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.00 % Favored : 94.95 % Rotamer: Outliers : 3.97 % Allowed : 19.26 % Favored : 76.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.20), residues: 2039 helix: 1.94 (0.15), residues: 1318 sheet: -0.08 (0.72), residues: 51 loop : -1.40 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP D 773 HIS 0.005 0.001 HIS A 310 PHE 0.018 0.001 PHE A 421 TYR 0.022 0.001 TYR D 810 ARG 0.004 0.000 ARG A 269 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4078 Ramachandran restraints generated. 2039 Oldfield, 0 Emsley, 2039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4078 Ramachandran restraints generated. 2039 Oldfield, 0 Emsley, 2039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 184 time to evaluate : 1.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 828 GLN cc_start: 0.6179 (OUTLIER) cc_final: 0.5728 (pt0) REVERT: D 893 LEU cc_start: 0.9102 (tp) cc_final: 0.8847 (tt) REVERT: D 894 GLU cc_start: 0.8205 (mp0) cc_final: 0.7973 (mp0) REVERT: A 213 MET cc_start: 0.8273 (mmt) cc_final: 0.7758 (mmt) REVERT: A 355 THR cc_start: 0.8938 (OUTLIER) cc_final: 0.8679 (m) REVERT: B 222 LEU cc_start: 0.7748 (OUTLIER) cc_final: 0.7210 (pp) REVERT: B 258 TYR cc_start: 0.5867 (OUTLIER) cc_final: 0.5134 (t80) REVERT: B 407 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7543 (mm-30) REVERT: B 415 ILE cc_start: 0.8466 (tp) cc_final: 0.8216 (tp) REVERT: B 611 ILE cc_start: 0.8009 (OUTLIER) cc_final: 0.7677 (pp) REVERT: C 397 MET cc_start: 0.8683 (tpp) cc_final: 0.8432 (mmt) outliers start: 62 outliers final: 34 residues processed: 225 average time/residue: 0.9869 time to fit residues: 255.0537 Evaluate side-chains 201 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 162 time to evaluate : 1.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 779 LEU Chi-restraints excluded: chain D residue 812 CYS Chi-restraints excluded: chain D residue 828 GLN Chi-restraints excluded: chain D residue 837 THR Chi-restraints excluded: chain D residue 922 LEU Chi-restraints excluded: chain D residue 980 PHE Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain D residue 1115 ILE Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 258 TYR Chi-restraints excluded: chain B residue 287 GLU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 318 SER Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 577 ASP Chi-restraints excluded: chain B residue 599 GLN Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain C residue 258 TYR Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 428 MET Chi-restraints excluded: chain C residue 449 ARG Chi-restraints excluded: chain C residue 504 ILE Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 571 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 66 optimal weight: 4.9990 chunk 177 optimal weight: 0.8980 chunk 38 optimal weight: 6.9990 chunk 115 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 197 optimal weight: 9.9990 chunk 163 optimal weight: 0.9990 chunk 91 optimal weight: 0.5980 chunk 16 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 103 optimal weight: 5.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 284 GLN B 494 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 15975 Z= 0.220 Angle : 0.550 8.969 21552 Z= 0.290 Chirality : 0.041 0.181 2275 Planarity : 0.003 0.055 2780 Dihedral : 4.743 58.837 2268 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.30 % Favored : 94.65 % Rotamer: Outliers : 4.22 % Allowed : 20.47 % Favored : 75.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.19), residues: 2039 helix: 1.96 (0.15), residues: 1317 sheet: 0.01 (0.75), residues: 46 loop : -1.42 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP D 773 HIS 0.005 0.001 HIS A 310 PHE 0.019 0.001 PHE A 421 TYR 0.020 0.001 TYR D 810 ARG 0.005 0.000 ARG A 269 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4078 Ramachandran restraints generated. 2039 Oldfield, 0 Emsley, 2039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4078 Ramachandran restraints generated. 2039 Oldfield, 0 Emsley, 2039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 172 time to evaluate : 1.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 828 GLN cc_start: 0.6217 (OUTLIER) cc_final: 0.5777 (pt0) REVERT: D 893 LEU cc_start: 0.9142 (tp) cc_final: 0.8892 (tt) REVERT: D 894 GLU cc_start: 0.8236 (mt-10) cc_final: 0.7988 (mp0) REVERT: D 1144 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.8359 (pt0) REVERT: A 213 MET cc_start: 0.8306 (mmt) cc_final: 0.7646 (mmt) REVERT: A 355 THR cc_start: 0.8964 (OUTLIER) cc_final: 0.8708 (m) REVERT: B 222 LEU cc_start: 0.7787 (OUTLIER) cc_final: 0.7265 (pp) REVERT: B 258 TYR cc_start: 0.5983 (OUTLIER) cc_final: 0.5160 (t80) REVERT: B 407 GLU cc_start: 0.7918 (mt-10) cc_final: 0.7594 (mm-30) REVERT: B 415 ILE cc_start: 0.8477 (tp) cc_final: 0.8256 (tp) REVERT: B 419 MET cc_start: 0.7280 (mtm) cc_final: 0.7076 (mtm) REVERT: C 303 MET cc_start: 0.8369 (ttm) cc_final: 0.8149 (ttt) REVERT: C 397 MET cc_start: 0.8680 (tpp) cc_final: 0.8385 (mmt) outliers start: 66 outliers final: 38 residues processed: 213 average time/residue: 0.9753 time to fit residues: 238.5391 Evaluate side-chains 203 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 160 time to evaluate : 1.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 779 LEU Chi-restraints excluded: chain D residue 828 GLN Chi-restraints excluded: chain D residue 906 ILE Chi-restraints excluded: chain D residue 980 PHE Chi-restraints excluded: chain D residue 1012 ASP Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain D residue 1115 ILE Chi-restraints excluded: chain D residue 1144 GLU Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 258 TYR Chi-restraints excluded: chain B residue 287 GLU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 318 SER Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 530 ILE Chi-restraints excluded: chain B residue 599 GLN Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 258 TYR Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 428 MET Chi-restraints excluded: chain C residue 449 ARG Chi-restraints excluded: chain C residue 504 ILE Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 599 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 190 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 112 optimal weight: 0.7980 chunk 144 optimal weight: 30.0000 chunk 111 optimal weight: 0.0970 chunk 166 optimal weight: 0.6980 chunk 110 optimal weight: 0.7980 chunk 196 optimal weight: 10.0000 chunk 123 optimal weight: 0.7980 chunk 119 optimal weight: 0.5980 chunk 90 optimal weight: 1.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 284 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15975 Z= 0.172 Angle : 0.538 9.100 21552 Z= 0.282 Chirality : 0.040 0.177 2275 Planarity : 0.003 0.056 2780 Dihedral : 4.633 57.586 2267 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.95 % Favored : 95.00 % Rotamer: Outliers : 3.58 % Allowed : 21.63 % Favored : 74.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.19), residues: 2039 helix: 2.00 (0.15), residues: 1318 sheet: 0.09 (0.75), residues: 46 loop : -1.36 (0.24), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP D 773 HIS 0.005 0.001 HIS A 310 PHE 0.023 0.001 PHE A 374 TYR 0.019 0.001 TYR D 810 ARG 0.007 0.000 ARG D1008 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4078 Ramachandran restraints generated. 2039 Oldfield, 0 Emsley, 2039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4078 Ramachandran restraints generated. 2039 Oldfield, 0 Emsley, 2039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 174 time to evaluate : 1.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 893 LEU cc_start: 0.9152 (tp) cc_final: 0.8918 (tt) REVERT: A 213 MET cc_start: 0.8280 (mmm) cc_final: 0.7690 (mmt) REVERT: A 355 THR cc_start: 0.8941 (OUTLIER) cc_final: 0.8678 (m) REVERT: B 203 TYR cc_start: 0.6361 (t80) cc_final: 0.5222 (t80) REVERT: B 222 LEU cc_start: 0.7764 (OUTLIER) cc_final: 0.7233 (pp) REVERT: B 258 TYR cc_start: 0.5943 (OUTLIER) cc_final: 0.5134 (t80) REVERT: B 407 GLU cc_start: 0.7899 (mt-10) cc_final: 0.7580 (mm-30) REVERT: B 415 ILE cc_start: 0.8465 (tp) cc_final: 0.8262 (tp) REVERT: C 303 MET cc_start: 0.8345 (ttm) cc_final: 0.8123 (ttt) outliers start: 56 outliers final: 36 residues processed: 210 average time/residue: 0.9829 time to fit residues: 236.5921 Evaluate side-chains 204 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 165 time to evaluate : 2.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 779 LEU Chi-restraints excluded: chain D residue 817 LEU Chi-restraints excluded: chain D residue 980 PHE Chi-restraints excluded: chain D residue 1012 ASP Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain D residue 1115 ILE Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 258 TYR Chi-restraints excluded: chain B residue 287 GLU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 318 SER Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 577 ASP Chi-restraints excluded: chain B residue 599 GLN Chi-restraints excluded: chain C residue 258 TYR Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 428 MET Chi-restraints excluded: chain C residue 449 ARG Chi-restraints excluded: chain C residue 504 ILE Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 599 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 121 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 chunk 59 optimal weight: 0.0970 chunk 38 optimal weight: 6.9990 chunk 125 optimal weight: 0.9990 chunk 133 optimal weight: 0.9990 chunk 97 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 154 optimal weight: 0.9980 chunk 178 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 599 GLN B 284 GLN B 494 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 15975 Z= 0.196 Angle : 0.552 9.913 21552 Z= 0.289 Chirality : 0.041 0.176 2275 Planarity : 0.003 0.056 2780 Dihedral : 4.597 56.572 2267 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.05 % Favored : 94.90 % Rotamer: Outliers : 3.45 % Allowed : 21.88 % Favored : 74.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.19), residues: 2039 helix: 2.02 (0.15), residues: 1313 sheet: 0.17 (0.75), residues: 46 loop : -1.34 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP D 773 HIS 0.005 0.001 HIS A 310 PHE 0.020 0.001 PHE A 421 TYR 0.018 0.001 TYR D 810 ARG 0.004 0.000 ARG A 269 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4078 Ramachandran restraints generated. 2039 Oldfield, 0 Emsley, 2039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4078 Ramachandran restraints generated. 2039 Oldfield, 0 Emsley, 2039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 171 time to evaluate : 1.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 828 GLN cc_start: 0.5954 (OUTLIER) cc_final: 0.5531 (pt0) REVERT: D 893 LEU cc_start: 0.9145 (tp) cc_final: 0.8917 (tt) REVERT: D 1117 GLN cc_start: 0.7861 (OUTLIER) cc_final: 0.6498 (tm-30) REVERT: D 1144 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.8382 (pt0) REVERT: A 213 MET cc_start: 0.8293 (mmm) cc_final: 0.7697 (mmt) REVERT: A 355 THR cc_start: 0.8948 (OUTLIER) cc_final: 0.8688 (m) REVERT: B 203 TYR cc_start: 0.6369 (t80) cc_final: 0.5224 (t80) REVERT: B 222 LEU cc_start: 0.7773 (OUTLIER) cc_final: 0.7244 (pp) REVERT: B 258 TYR cc_start: 0.6041 (OUTLIER) cc_final: 0.5206 (t80) REVERT: B 407 GLU cc_start: 0.7899 (mt-10) cc_final: 0.7582 (mm-30) REVERT: B 415 ILE cc_start: 0.8452 (tp) cc_final: 0.8233 (tp) REVERT: B 532 GLN cc_start: 0.6265 (mm-40) cc_final: 0.5988 (mm-40) REVERT: C 303 MET cc_start: 0.8354 (ttm) cc_final: 0.8136 (ttt) outliers start: 54 outliers final: 36 residues processed: 206 average time/residue: 1.0270 time to fit residues: 242.8039 Evaluate side-chains 207 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 165 time to evaluate : 1.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 779 LEU Chi-restraints excluded: chain D residue 828 GLN Chi-restraints excluded: chain D residue 980 PHE Chi-restraints excluded: chain D residue 1012 ASP Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain D residue 1115 ILE Chi-restraints excluded: chain D residue 1117 GLN Chi-restraints excluded: chain D residue 1144 GLU Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 258 TYR Chi-restraints excluded: chain B residue 287 GLU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 318 SER Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 530 ILE Chi-restraints excluded: chain B residue 599 GLN Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 258 TYR Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 428 MET Chi-restraints excluded: chain C residue 449 ARG Chi-restraints excluded: chain C residue 504 ILE Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 571 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 188 optimal weight: 3.9990 chunk 171 optimal weight: 0.8980 chunk 183 optimal weight: 0.6980 chunk 110 optimal weight: 0.9980 chunk 79 optimal weight: 0.8980 chunk 143 optimal weight: 0.7980 chunk 56 optimal weight: 0.2980 chunk 165 optimal weight: 0.3980 chunk 173 optimal weight: 2.9990 chunk 182 optimal weight: 0.9980 chunk 120 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 284 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 15975 Z= 0.183 Angle : 0.562 11.070 21552 Z= 0.292 Chirality : 0.041 0.176 2275 Planarity : 0.003 0.056 2780 Dihedral : 4.550 55.908 2267 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.95 % Favored : 95.00 % Rotamer: Outliers : 3.33 % Allowed : 21.94 % Favored : 74.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.20), residues: 2039 helix: 2.03 (0.15), residues: 1314 sheet: 0.25 (0.76), residues: 46 loop : -1.29 (0.24), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP D 773 HIS 0.005 0.001 HIS A 310 PHE 0.025 0.001 PHE A 374 TYR 0.018 0.001 TYR D 810 ARG 0.004 0.000 ARG A 269 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4078 Ramachandran restraints generated. 2039 Oldfield, 0 Emsley, 2039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4078 Ramachandran restraints generated. 2039 Oldfield, 0 Emsley, 2039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 174 time to evaluate : 1.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 828 GLN cc_start: 0.5904 (OUTLIER) cc_final: 0.5510 (pt0) REVERT: D 893 LEU cc_start: 0.9139 (tp) cc_final: 0.8906 (tt) REVERT: D 1117 GLN cc_start: 0.7797 (OUTLIER) cc_final: 0.6371 (tm-30) REVERT: D 1144 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.8380 (pt0) REVERT: A 213 MET cc_start: 0.8264 (mmm) cc_final: 0.7701 (mmt) REVERT: A 355 THR cc_start: 0.8937 (OUTLIER) cc_final: 0.8670 (m) REVERT: B 203 TYR cc_start: 0.6431 (t80) cc_final: 0.5215 (t80) REVERT: B 222 LEU cc_start: 0.7760 (OUTLIER) cc_final: 0.7227 (pp) REVERT: B 258 TYR cc_start: 0.6031 (OUTLIER) cc_final: 0.5246 (t80) REVERT: B 263 TRP cc_start: 0.7683 (t-100) cc_final: 0.7167 (t-100) REVERT: B 279 MET cc_start: 0.7790 (ptm) cc_final: 0.7150 (ptm) REVERT: B 407 GLU cc_start: 0.7885 (mt-10) cc_final: 0.7564 (mm-30) REVERT: B 532 GLN cc_start: 0.6358 (mm-40) cc_final: 0.6073 (mm-40) REVERT: C 303 MET cc_start: 0.8343 (ttm) cc_final: 0.8121 (ttt) outliers start: 52 outliers final: 39 residues processed: 208 average time/residue: 1.0121 time to fit residues: 240.3448 Evaluate side-chains 211 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 166 time to evaluate : 1.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 779 LEU Chi-restraints excluded: chain D residue 828 GLN Chi-restraints excluded: chain D residue 980 PHE Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain D residue 1115 ILE Chi-restraints excluded: chain D residue 1117 GLN Chi-restraints excluded: chain D residue 1144 GLU Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 258 TYR Chi-restraints excluded: chain B residue 287 GLU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 318 SER Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 577 ASP Chi-restraints excluded: chain B residue 599 GLN Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 258 TYR Chi-restraints excluded: chain C residue 263 TRP Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 428 MET Chi-restraints excluded: chain C residue 449 ARG Chi-restraints excluded: chain C residue 503 TYR Chi-restraints excluded: chain C residue 504 ILE Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 571 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 193 optimal weight: 7.9990 chunk 118 optimal weight: 0.0170 chunk 91 optimal weight: 0.6980 chunk 134 optimal weight: 4.9990 chunk 203 optimal weight: 4.9990 chunk 187 optimal weight: 6.9990 chunk 161 optimal weight: 1.9990 chunk 16 optimal weight: 9.9990 chunk 125 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 128 optimal weight: 0.5980 overall best weight: 1.0622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 599 GLN B 284 GLN B 494 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.1644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 15975 Z= 0.224 Angle : 0.583 10.815 21552 Z= 0.304 Chirality : 0.042 0.199 2275 Planarity : 0.004 0.055 2780 Dihedral : 4.577 55.903 2267 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.20 % Favored : 94.75 % Rotamer: Outliers : 3.07 % Allowed : 22.07 % Favored : 74.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.20), residues: 2039 helix: 2.01 (0.15), residues: 1313 sheet: 0.21 (0.76), residues: 46 loop : -1.30 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.002 TRP D 783 HIS 0.005 0.001 HIS A 310 PHE 0.020 0.001 PHE A 421 TYR 0.030 0.001 TYR C 503 ARG 0.005 0.000 ARG A 269 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4078 Ramachandran restraints generated. 2039 Oldfield, 0 Emsley, 2039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4078 Ramachandran restraints generated. 2039 Oldfield, 0 Emsley, 2039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 169 time to evaluate : 2.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 828 GLN cc_start: 0.5920 (OUTLIER) cc_final: 0.5529 (pt0) REVERT: D 893 LEU cc_start: 0.9132 (tp) cc_final: 0.8907 (tt) REVERT: D 1117 GLN cc_start: 0.7800 (OUTLIER) cc_final: 0.6361 (tm-30) REVERT: D 1144 GLU cc_start: 0.8637 (OUTLIER) cc_final: 0.8427 (pt0) REVERT: A 213 MET cc_start: 0.8281 (mmm) cc_final: 0.7686 (mmt) REVERT: A 355 THR cc_start: 0.8957 (OUTLIER) cc_final: 0.8697 (m) REVERT: B 203 TYR cc_start: 0.6373 (t80) cc_final: 0.5221 (t80) REVERT: B 222 LEU cc_start: 0.7777 (OUTLIER) cc_final: 0.7262 (pp) REVERT: B 258 TYR cc_start: 0.6069 (OUTLIER) cc_final: 0.5254 (t80) REVERT: B 263 TRP cc_start: 0.7635 (t-100) cc_final: 0.7135 (t-100) REVERT: B 279 MET cc_start: 0.7821 (ptm) cc_final: 0.7208 (ptm) REVERT: B 407 GLU cc_start: 0.7891 (mt-10) cc_final: 0.7568 (mm-30) REVERT: B 532 GLN cc_start: 0.6428 (mm-40) cc_final: 0.6158 (mm-40) REVERT: C 303 MET cc_start: 0.8356 (ttm) cc_final: 0.8134 (ttt) outliers start: 48 outliers final: 37 residues processed: 202 average time/residue: 1.0572 time to fit residues: 243.4242 Evaluate side-chains 206 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 163 time to evaluate : 1.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 779 LEU Chi-restraints excluded: chain D residue 828 GLN Chi-restraints excluded: chain D residue 980 PHE Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain D residue 1115 ILE Chi-restraints excluded: chain D residue 1117 GLN Chi-restraints excluded: chain D residue 1144 GLU Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 258 TYR Chi-restraints excluded: chain B residue 287 GLU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 318 SER Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 530 ILE Chi-restraints excluded: chain B residue 599 GLN Chi-restraints excluded: chain C residue 213 MET Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 258 TYR Chi-restraints excluded: chain C residue 263 TRP Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 428 MET Chi-restraints excluded: chain C residue 449 ARG Chi-restraints excluded: chain C residue 504 ILE Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 571 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 149 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 44 optimal weight: 9.9990 chunk 162 optimal weight: 0.7980 chunk 67 optimal weight: 0.0000 chunk 166 optimal weight: 0.3980 chunk 20 optimal weight: 4.9990 chunk 29 optimal weight: 0.6980 chunk 142 optimal weight: 1.9990 overall best weight: 0.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 284 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.139278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.105018 restraints weight = 27335.317| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 2.78 r_work: 0.3498 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 15975 Z= 0.175 Angle : 0.570 10.184 21552 Z= 0.296 Chirality : 0.041 0.204 2275 Planarity : 0.003 0.056 2780 Dihedral : 4.389 55.116 2265 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.81 % Favored : 95.14 % Rotamer: Outliers : 2.62 % Allowed : 22.65 % Favored : 74.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.20), residues: 2039 helix: 2.08 (0.15), residues: 1308 sheet: 0.31 (0.77), residues: 46 loop : -1.22 (0.24), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.002 TRP D 783 HIS 0.005 0.001 HIS A 310 PHE 0.033 0.001 PHE A 374 TYR 0.018 0.001 TYR D 810 ARG 0.004 0.000 ARG A 269 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5035.35 seconds wall clock time: 92 minutes 8.37 seconds (5528.37 seconds total)